I don't put plastic in the microwave for any food. Would never for a baby bottle. We used a warmer, putting the bottle in a glass of hot water, or we heated in the microwave in a glass measuring cup, swished around and then transferred to the bottle.
Buy a big wide-mouthed mug. Fill the mug about 2/3 with water and heat it in the microwave till the water is pretty hot. Then put the bottle in the mug for a couple minutes, then shake before testing and serving.
I don't know if it affects the chemistry of the fomula, but I don't think it will impact the bottle. We used a microwave bottle sterilizer, and I can't see how heating milk in the microwave would be any different in terms of how it affects the bottle.
If you haven't tried room temp yet, though, I would advise trying it. DD didn't seem to distinguish room temp from heated at all, and it was so much easier!
OP here -- for the hotspots concern, I would wait, and gently swish around, to dissipate any possible such spots. Again, I am curious if others do microwave, and have not had issues.
The only statement of caution in the instructions for the bottle type we're using (Dr. Brown's) is that microwaving may create hotspots in the liquid. At first, we were heating the bottles (for formula) indirectly, by placing into a vessel holding boiled water. Then we tried the microwave, and no surprise that it heats the fluid very quickly. For other plastic bottle users, do you also use the microwave? I have some worry that we used to do it perhaps the safer way, but I do hope that microwave heating (for formula only; for breast milk I have read that microwaving may break down proteins) is not causing any harm (either to the liquid itself or indirectly, by affecting the bottle integrity somehow).